{ "_id": "6a22e832530b9bc726bcb5c2", "Package": "FastJM", "Type": "Package", "Title": "Semi-Parametric Joint Modeling of Longitudinal and Survival Data", "Version": "1.7.0", "Date": "2026-05-26", "Authors@R": "c(\nperson(\"Shanpeng\", \"Li\", email = \"lishanpeng0913@ucla.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Ace\", \"Mejia-Sanchez\", email = \"aceisabel.mejiasanchez1@ucr.edu\",\nrole = \"ctb\"),\nperson(\"Emily\", \"Ouyang\", email = \"eouya001@ucr.edu\",\nrole = \"ctb\"),\nperson(\"Gang\", \"Li\", email = \"vli@ucla.edu\",\nrole = \"ctb\")\n)", "Maintainer": "Shanpeng Li ", "Encoding": "UTF-8", "Description": "Implements scalable joint models for large-scale competing\nrisks time-to-event data with one or multiple longitudinal\nbiomarkers using the efficient algorithms developed by Li et\nal. (2022) and\n. The time-to-event process is\nmodeled using a cause-specific Cox proportional hazards model\nwith time-fixed covariates, while longitudinal biomarkers are\nmodeled using linear mixed-effects models. The association\nbetween the longitudinal and survival processes is captured\nthrough shared random effects. The package enables analysis of\nlarge-scale biomedical data to model biomarker trajectories,\nestimate their effects on event risks, and perform dynamic\nprediction of future events based on patients' longitudinal\nhistories. Functions for simulating survival and longitudinal\ndata for multiple biomarkers are included, along with built-in\nexample datasets. The package also supports modeling a single\nbiomarker with heterogeneous within-subject variability via\nfunctionality adapted from the 'JMH' package.", "License": "GPL (>= 3)", "NeedsCompilation": "yes", "RoxygenNote": "7.3.2", "LazyData": "true", "Packaged": { "Date": "2026-06-05 14:52:13 UTC", "User": "root" }, "VignetteBuilder": "knitr", "Language": "en-US", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev libnode-dev", "Repository": "https://shanpengli.r-universe.dev", "Date/Publication": "2026-06-05 12:52:44 UTC", "RemoteUrl": "https://github.com/shanpengli/fastjm", "RemoteRef": "HEAD", "RemoteSha": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "Author": "Shanpeng Li [aut, cre],\nAce Mejia-Sanchez [ctb],\nEmily Ouyang [ctb],\nGang Li [ctb]", "MD5sum": "c15a5aecb75dab7aefddde8d2294b442", "_user": "shanpengli", "_type": "src", "_file": "FastJM_1.7.0.tar.gz", "_fileid": "b63c561491a5f86b3ff14e69f22e3bb3fc97e85ea7db0d16a80ef16ea2f43d61", "_filesize": 1056653, "_sha256": "b63c561491a5f86b3ff14e69f22e3bb3fc97e85ea7db0d16a80ef16ea2f43d61", "_created": "2026-06-05T14:52:13.000Z", "_published": "2026-06-05T15:16:02.299Z", "_distro": "noble", "_jobs": [ { "job": 79753726420, "time": 650, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7439960489" }, { "job": 79753726464, "time": 713, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7439983509" }, { "job": 79753726392, "time": 687, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7439973976" }, { "job": 79753726390, "time": 680, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7439970630" }, { "job": 79753726378, "time": 554, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7439920419" }, { "job": 79753726499, "time": 898, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7440052455" }, { "job": 79753726377, "time": 597, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7439938342" }, { "job": 79753726402, "time": 971, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7440078358" }, { "job": 79750375269, "time": 1065, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7439710796" }, { "job": 79753726343, "time": 389, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7439858956" }, { "job": 79753726366, "time": 894, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7440051208" }, { "job": 79753726411, "time": 918, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7440059505" }, { "job": 79753726373, "time": 886, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7440047725" } ], "_buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/shanpengli/fastjm", "_commit": { "id": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "author": "Emily Ouyang ", "committer": "Emily Ouyang ", "message": "update for diff latAsso\n", "time": 1780663964 }, "_maintainer": { "name": "Shanpeng Li", "email": "lishanpeng0913@ucla.edu", "login": "shanpengli", "description": "Ph.D. in Biostatistics", "uuid": 18046660 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "survival", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "statmod", "role": "Depends" }, { "package": "magrittr", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.7", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "nlme", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "pec", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "tidycmprsk", "role": "Imports" }, { "package": "rlang", "version": ">= 0.4.11", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "shanpengli", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-23", "n": 3 }, { "week": "2025-24", "n": 1 }, { "week": "2025-25", "n": 12 }, { "week": "2025-30", "n": 2 }, { "week": "2025-35", "n": 1 }, { "week": "2025-40", "n": 4 }, { "week": "2025-41", "n": 4 }, { "week": "2025-42", "n": 9 }, { "week": "2025-43", "n": 4 }, { "week": "2025-45", "n": 12 }, { "week": "2026-02", "n": 1 }, { "week": "2026-05", "n": 2 }, { "week": "2026-13", "n": 1 }, { "week": "2026-21", "n": 5 }, { "week": "2026-22", "n": 3 }, { "week": "2026-23", "n": 3 } ], "_tags": [ { "name": "V1.5.2", "date": "2025-10-18" } ], "_topics": [ "cpp", "cpp" ], "_stars": 7, "_contributors": [ { "user": "shanpengli", "count": 72, "uuid": 18046660 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 } ], "_userbio": { "uuid": 18046660, "type": "user", "name": "Shanpeng Li", "description": "Ph.D. in Biostatistics" }, "_downloads": { "count": 579, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FastJM" }, "_devurl": "https://github.com/shanpengli/fastjm", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FastJM.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/shanpengli/fastjm", "_realowner": "shanpengli", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-01-06" }, { "version": "1.0.1", "date": "2022-01-12" }, { "version": "1.1.0", "date": "2022-02-08" }, { "version": "1.1.1", "date": "2022-02-14" }, { "version": "1.1.2", "date": "2022-02-16" }, { "version": "1.1.3", "date": "2022-06-01" }, { "version": "1.2.0", "date": "2022-08-06" }, { "version": "1.3.1", "date": "2023-03-26" }, { "version": "1.4.0", "date": "2023-10-10" }, { "version": "1.4.1", "date": "2024-01-09" }, { "version": "1.4.2", "date": "2024-03-01" }, { "version": "1.5.0", "date": "2025-06-22" }, { "version": "1.5.1", "date": "2025-07-24" }, { "version": "1.5.2", "date": "2025-10-18" }, { "version": "1.5.3", "date": "2025-11-08" }, { "version": "1.6.0", "date": "2026-03-28" } ], "_exports": [ "combine_biomarkers", "Concordance.jmcs", "Concordance.JMMLSM", "DynPredAcc", "fixef", "jmcs", "jmcs_control", "JMMLSM", "JMMLSM_control", "mvjmcs", "mvjmcs_control", "ranef", "simJMWSVdata", "simmvJMdata", "survfitJM", "survfitjmcs", "survfitJMMLSM", "survfitmvjmcs", "timeplot" ], "_datasets": [ { "name": "cdata", "title": "Simulated competing risks data correlated with ydata", "object": "cdata", "class": [ "data.frame" ], "fields": [ "ID", "surv", "failure_type", "x1", "x2", "gender", "race" ], "rows": 1000, "table": true, "tojson": true }, { "name": "cdatah", "title": "Simulated competing risks data where event hazards depend on within-subject variance", "object": "cdatah", "class": [ "data.frame" ], "fields": [ "ID", "survtime", "cmprsk", "var1", "var2", "var3" ], "rows": 200, "table": true, "tojson": true }, { "name": "mvcdata", "title": "Simulated competing risks data correlated with mvydata", "object": "mvcdata", "class": [ "data.frame" ], "fields": [ "ID", "survtime", "cmprsk", "X21", "X22" ], "rows": 800, "table": true, "tojson": true }, { "name": "mvydata", "title": "Simulated bivariate longitudinal data", "object": "mvydata", "class": [ "data.frame" ], "fields": [ "ID", "time", "Y1", "Y2", "X11", "X12" ], "rows": 5645, "table": true, "tojson": true }, { "name": "ydata", "title": "Simulated longitudinal data", "object": "ydata", "class": [ "data.frame" ], "fields": [ "ID", "response", "time", "x1", "gender", "race" ], "rows": 3067, "table": true, "tojson": true }, { "name": "ydatah", "title": "Simulated longitudinal data with within-subject variance", "object": "ydatah", "class": [ "data.frame" ], "fields": [ "ID", "Y", "time", "Z1", "Z2", "Z3" ], "rows": 1353, "table": true, "tojson": true } ], "_help": [ { "page": "cdata", "title": "Simulated competing risks data correlated with ydata", "topics": [ "cdata" ] }, { "page": "cdatah", "title": "Simulated competing risks data where event hazards depend on within-subject variance", "topics": [ "cdatah" ] }, { "page": "combine_biomarkers", "title": "Combine biomarker measurements across multiple data frames", "topics": [ "combine_biomarkers" ] }, { "page": "Concordance", "title": "Concordance for joint models", "topics": [ "Concordance", "Concordance.jmcs", "Concordance.JMMLSM" ] }, { "page": "DynPredAcc", "title": "Dynamic prediction accuracy metrics for joint models", "topics": [ "DynPredAcc" ] }, { "page": "fitted", "title": "Fitted values for joint models", "topics": [ "fitted", "fitted.jmcs" ] }, { "page": "fixef", "title": "Estimated coefficients estimates for joint models", "topics": [ "fixef" ] }, { "page": "jmcs", "title": "Joint modeling of longitudinal continuous data and competing risks", "topics": [ "jmcs" ] }, { "page": "jmcs_control", "title": "Control Options for jmcs", "topics": [ "jmcs_control" ] }, { "page": "JMMLSM", "title": "Joint Modeling for Continuous Outcomes", "topics": [ "JMMLSM" ] }, { "page": "JMMLSM_control", "title": "Control Options for JMMLSM", "topics": [ "JMMLSM_control" ] }, { "page": "mvcdata", "title": "Simulated competing risks data correlated with mvydata", "topics": [ "mvcdata" ] }, { "page": "mvjmcs", "title": "Joint modeling of multivariate longitudinal and competing risks data", "topics": [ "mvjmcs" ] }, { "page": "mvjmcs_control", "title": "Control Options for mvjmcs", "topics": [ "mvjmcs_control" ] }, { "page": "mvydata", "title": "Simulated bivariate longitudinal data", "topics": [ "mvydata" ] }, { "page": "plot.jmcs", "title": "Fitted values for joint models", "topics": [ "plot.jmcs" ] }, { "page": "plot.survfitJMMLSM", "title": "Plot conditional probabilities for new subjects", "topics": [ "plot.survfitJMMLSM" ] }, { "page": "print", "title": "Print jmcs", "topics": [ "print", "print.jmcs", "print.mvjmcs" ] }, { "page": "print.JMMLSM", "title": "Print JMMLSM", "topics": [ "print.JMMLSM" ] }, { "page": "print.survfitjmcs", "title": "Print survfitjmcs", "topics": [ "print.survfitjmcs" ] }, { "page": "print.survfitJMMLSM", "title": "Print survfitJMMLSM", "topics": [ "print.survfitJMMLSM" ] }, { "page": "print.survfitmvjmcs", "title": "Print survfitmvjmcs", "topics": [ "print.survfitmvjmcs" ] }, { "page": "ranef", "title": "Random effects estimates for joint models", "topics": [ "ranef" ] }, { "page": "residuals", "title": "Residuals for joint models", "topics": [ "residuals", "residuals.jmcs" ] }, { "page": "simJMWSVdata", "title": "Simulate joint model data with heterogeneous within-subject variability", "topics": [ "simJMWSVdata" ] }, { "page": "simmvJMdata", "title": "Joint modeling of multivariate longitudinal and competing risks data", "topics": [ "simmvJMdata" ] }, { "page": "summary", "title": "Print ConcordanceJMMLSM", "topics": [ "summary", "summary.Concordancejmcs", "summary.ConcordanceJMMLSM", "summary.DynPredAcc", "summary.jmcs", "summary.JMMLSM", "summary.mvjmcs" ] }, { "page": "survfitJM", "title": "Dynamic predictions from fitted joint models", "topics": [ "survfitJM", "survfitJM.jmcs", "survfitJM.JMMLSM", "survfitJM.mvjmcs" ] }, { "page": "survfitjmcs", "title": "Prediction in Joint Models", "topics": [ "survfitjmcs" ] }, { "page": "survfitJMMLSM", "title": "Prediction in Joint Models", "topics": [ "survfitJMMLSM" ] }, { "page": "survfitmvjmcs", "title": "Prediction in Joint Models", "topics": [ "survfitmvjmcs" ] }, { "page": "timeplot", "title": "Diagnostic plots for the fitted joint model", "topics": [ "timeplot" ] }, { "page": "vcov", "title": "Variance-covariance matrix of the estimated parameters for joint models", "topics": [ "vcov", "vcov.jmcs", "vcov.JMMLSM", "vcov.mvjmcs" ] }, { "page": "ydata", "title": "Simulated longitudinal data", "topics": [ "ydata" ] }, { "page": "ydatah", "title": "Simulated longitudinal data with within-subject variance", "topics": [ "ydatah" ] } ], "_readme": "https://github.com/shanpengli/fastjm/raw/HEAD/README.md", "_rundeps": [ "backports", "base64enc", "bigD", "bitops", "broom", "bslib", "cachem", "cards", "cardx", "caret", "checkmate", "class", "cli", "clock", "cluster", "cmprsk", "codetools", "colorspace", "commonmark", "cpp11", "curl", "data.table", "diagram", "digest", "doParallel", "dplyr", "e1071", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "foreign", "Formula", "fs", "future", "future.apply", "generics", "ggplot2", "glmnet", "globals", "glue", "gower", "gridExtra", "gt", "gtable", "gtsummary", "hardhat", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "ipred", "isoband", "iterators", "jquerylib", "jsonlite", "juicyjuice", "KernSmooth", "knitr", "labeling", "lattice", "lava", "lifecycle", "listenv", "litedown", "lubridate", "magrittr", "markdown", "MASS", "Matrix", "MatrixModels", "memoise", "mets", "mime", "ModelMetrics", "multcomp", "mvtnorm", "nlme", "nnet", "numDeriv", "parallelly", "pec", "pillar", "pkgconfig", "plotrix", "plyr", "polspline", "pROC", "prodlim", "progressr", "proxy", "Publish", "purrr", "quantreg", "R6", "ranger", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "reactable", "reactR", "recipes", "reshape2", "riskRegression", "rlang", "rmarkdown", "rms", "rpart", "rstudioapi", "S7", "sandwich", "sass", "scales", "shape", "SparseM", "sparsevctrs", "SQUAREM", "statmod", "stringi", "stringr", "survival", "TH.data", "tibble", "tidycmprsk", "tidyr", "tidyselect", "timechange", "timeDate", "timereg", "tinytex", "tzdb", "utf8", "V8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 5.605520523437469, "_indexed": true, "_nocasepkg": "fastjm", "_universes": [ "shanpengli" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.0", "date": "2026-06-05T15:01:58.000Z", "distro": "noble", "arch": "aarch64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "6b081a00d9ffed34ece20325a2a455bf4430511b1f9b75ffc60aebb40d95fe3e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.7.0", "os": "linux", "version": "1.7.0", "date": "2026-06-05T15:01:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "21293d7886502661a9d81fb420ecba3ac7093fed8b838ca09633a27282ca9770", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "linux", "version": "1.7.0", "date": "2026-06-05T15:02:30.000Z", "distro": "noble", "arch": "aarch64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "5952cda1c68ddb54094e5b3c038fbc817cbc7c43620ef170a83a05565d7e8c9c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "linux", "version": "1.7.0", "date": "2026-06-05T15:01:51.000Z", "distro": "noble", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "34222bae66bcfaa1d528e2932895f4e777d29662fae800699152b05211830228", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0", "date": "2026-06-05T15:00:58.000Z", "arch": "aarch64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "1b03b613ee2d67b1df20e2e950857e7a477430c0758e65c4d9f143e41eb5a983", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0", "date": "2026-06-05T15:02:31.000Z", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "344cb2deb4c97e2f45186b7d5234c6dbeee0d3f74697ccdfec1ecf50f1cc5bf0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "mac", "version": "1.7.0", "date": "2026-06-05T15:01:11.000Z", "arch": "aarch64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "3e9dd93c813eda8ce82c810b10330da8f6fddbe3a0a24c161602ce38764308d1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "mac", "version": "1.7.0", "date": "2026-06-05T15:02:27.000Z", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "4286c223a622c8c736c006b3677b062eaab8bd34b730620ddc3d2e38dd26bf42", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.0", "date": "2026-06-05T15:01:42.000Z", "arch": "emscripten", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "6228ac3b8be8aa4e8dff18b107e7247c4bb71544f2babfbf82c53d4fb839e7ea", "status": "success", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.7.0", "os": "win", "version": "1.7.0", "date": "2026-06-05T15:00:41.000Z", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "0dc8f4db31f988357e3c73731e72afa4433f4c969d9981f14245afb9899efa39", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.5.3", "os": "win", "version": "1.7.0", "date": "2026-06-05T15:00:48.000Z", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "352172cccc8b66ff3a9f42120c086a31b944bd35c0ae5e409c21a9cfd0d88ea0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" }, { "r": "4.6.0", "os": "win", "version": "1.7.0", "date": "2026-06-05T15:00:49.000Z", "arch": "x86_64", "commit": "fc1ee0051c7edba2ebe4fea2a571143b712a34de", "fileid": "a1a021226d30e4f4c17a959aaa8d26384782a3474173ff947f0c945b6b7bde82", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/27021488543" } ] }